[R-sig-Geo] overlapping polygons in shapefile

Tue Mar 11 20:56:02 CET 2014

On Tue, 11 Mar 2014, Alice C. Hughes wrote:

> Hi All
> This should be simple-but ArcGis keeps getting stuck at 22%...I have a 
> large shapefile, which contains multiple overlapping polygons for 
> various species-and I would like to count for any area how many polygons 
> overlap.A script would be really fantastic!Thanks in advance

Wouldn't it just? However, as usual, such scripts will only cause grief, 
as they will not (necessarily) match your workflow. Most likely, you 
have two choices, one to rasterise thr polygons separately (not 
together, because they overlap), then count overlapping cells.

If the shapefile is "large", like tens of thousands of polygons, you could 
try the rgeos package, first using gUnarySTRtreeQuery() or 
gBinarySTRtreeQuery() to identify possible overlapping candidates (these 
functions report intersecting bounding boxes of polygons).

Next try gOverlaps() subsetting the input objects by the output of the 
intersecting bounding boxes. Once you've found the overlaps, take their 
intersections with gIntersection(), and get the area with gArea(). Note 
that this only applies to planar, projected polygons. If they are in 
geographical coordinates, project before using gArea(). Look carefully at 
the byid= arguments in gOverlaps, gIntersection and gArea. Depending on 
the complexity of the setting, you may be using for loops and subsetting 
by indices - there are examples in Ch. 5 of ASDAR (2nd edition) of this 
kind of subsetting (or see the online code at www.asdar-book.org), about 
chunks 41-3 in http://www.asdar-book.org/book2ed/cm2_mod.R.

Hope this helps,

Roger

> Alice
>
> Alice C. HughesAssociate ProfessorCentre for Integrative 
> Conservation,Xishuangbanna Tropical Botanical Garden,Chinese Academy of 
> SciencesMenglun, Mengla, Yunnan 666303, P.R. ChinaPh: 
> 15198676559achughes at xtbg.ac.cn
>
> Date: Mon, 6 May 2013 14:33:29 +1000
> Subject: Re: [Trop-R] Kernel Density Estimation Bootstrap
> From: lhodgson86 at gmail.com
> To: tropical-r at googlegroups.com
>
> Hi Christian,
> This formatting shows that the data has been read in as a single column with 'V1' as the column name and 'x,y' as the value of row 1, and so on:
>
>> test<-read.table("test.csv")> test
>                V11              x,y
> 2   648501,89104003   641686,8917264
> 4   645984,89143285   647058,8913794
> 6   649659,89129257   649613,8912828
> .....
>
> You can check how many columns there are in a data frame using 'ncol':
>
> ncol(test)
> To troubleshoot, I would first try using read.csv:
>
> test=read.csv(test,as.is=TRUE)ncol(test)
>
> If this does not give you two columns, then I would check that the file really is in standard .csv format.
>
> Lauren
>
> On Mon, May 6, 2013 at 1:17 PM, Christian Gredzens <christian.gredzens at my.jcu.edu.au> wrote:
>
> Leila,
>
> Thanks for your reply. I'm using likelihood cross validation (CVh) instead of least squares cross validation (LSCV). To my knowledge adehabitatHR doesn't run CVh so I think I will need to write a script or find another program which can calculate CVh.
>
>
> I used GME from spatialecology.com to calculate all of my KDEs, but I don't think GME runs bootstrapping. So I'm trying to run it through the bootstrapping package in R. Here is what I need to do:
>
>
> 1) Create my spatial points layer
> =mydata
>
> 2) Run the bootstrapping script:
>
>> mydataboot<-boot(mydata, (KDE script), R=1000)
>
> mydata= my spatial points file
> (KDE script)= what formula to run the bootstrap on
>
> R=1000 = the number of iterations I would like to run
>
> The issue I'm having is getting the bootstrapping script to run the KDE formula=(KDE script)
>
> Cheers,
> Christian
>
> On Friday, May 3, 2013 12:58:55 AM UTC-7, Leila Brook wrote:
> Hi Christian,
>
> There is a package called adehabitatHR that does kernel density estimation with LSCV bandwidth using a function called kernelUD(). I don't know if this will is similar to what you want? You will need to have the data in UTM and in SpatialPoints or SpatialPointsDataFrame format, which you can do using the sp package.
>
>
>
> There is a great vignette for adehabitatHR that will help with data formatting and running the KDE. I  exported the utilisation distribution for ArcGIS using writeRaster() in the raster package, but you can also export as contours.
>
>
>
> Cheers
>
> Leila
>
>
>
> ________________________________________
>
> From: tropi... at googlegroups.com [tropi... at googlegroups.com] on behalf of Stewart Macdonald [stewartm... at gmail.com]
>
> Sent: Friday, 3 May 2013 5:12 PM
>
> To: tropi... at googlegroups.com
>
> Subject: Re: [Trop-R] Kernel Density Estimation Bootstrap
>
>
>
> Hi Christian,
>
>
>
> What sort of data are you trying to import? A series of lat/longs that are in a text (or Excel) file? If so, the rGDAL library can be used to create spatial points:
>
>
>
> ###############
>
> library(rgdal)
>
> # if you don't already have this installed, you can do: install.packages('rgdal')
>
>
>
> # read in the data from a tab-delimited text file that has a header line
>
> rawPoints <- read.table('/data.csv', header=TRUE, sep='\t')
>
>
>
> # format as a SpatialPoint class and define the projection/datum (WGS84)
>
> q <- cbind(rawPoints$recordLon, rawPoints$recordLat)
>
> colnames(q) <- c("x", "y")
>
> qqq <- SpatialPoints(q, proj4string=CRS("+init=epsg:4326"))
>
> ###############
>
>
>
> Note: the above is a copied-and-pasted fragment from a working script of mine. I assume this fragment will work for you.
>
>
>
> I can't help you with your second question, and the answer to your third question will depend on the format of the bootstrap data (e.g., more points, polygons, raster).
>
>
>
>
>
> Hope this helps,
>
>
>
> Stewart
>
>
>
>
>
>
>
>
>
> On 03/05/2013, at 4:57 PM, Christian Gredzens <christian... at my.jcu.edu.au> wrote:
>
>
>
>> Hi All,
>
>>
>
>> I would like to run a bootstrap within R on a spatial dataset using a kernel density estimation function. Can anyone help me with this? I am new to R and thus have very little experience. It seems relatively easy to run the actual bootstrap but I am having problems in the following areas:
>
>>
>
>> 1) I don't know how to import spatial data into R and assign it an appropriate projection
>
>> 2) I need to setup a kernel function using a specific bandwidth (likelihood cross-validation (CVh)) and create the script so it will run within the bootstrap script
>
>> 3) I need to export the bootstrap data as an ArcGIS 10 file.
>
>>
>
>> Best Regards,
>
>> Christian Gredzens
>
>>
>
>> Christian Gredzens
>
>> MSc Student
>
>> School of Marine and Tropical Biology
>
>> James Cook University
>
>> Townsville, QLD, Australia 4811
>
>> Christian... at my.jcu.edu.au
>
>> Phone: 04 3875 3652
>
>>
>
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-- 
Roger Bivand
Department of Economics, Norwegian School of Economics,
Helleveien 30, N-5045 Bergen, Norway.
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